[Shadowstar]

It's sci-fi, the rules are about as malleable as wet clay. You can pretty much explain just about any gameplay-centric fix with a sci-fi explanation without too much effort. The focus should always be gameplay first.

In most sci-fi, ships in combat use thrusters or a sublight mode of thier engines rather than thier high-power long-distance engines (you don't constantly warp from place to place in Star Fleet Battles). These engines or modes could have a different fuel supply or a different system for burning supplies. However, using the SFB comparison, there is the potential to mod the game to include special abilities in combat, such as a one-shot "Picard maneuver" or somesuch... This would reflect a different system being used for long-distance travel than for combat, but allowing the system to be flexible enough that the rules can be bent a little in order to add a little something extra to gameplay.